Three British Muslims were today cleared of helping the 7 July bombers choose their targets by carrying out a reconnaissance mission in London seven months before the attacks that killed 52 people and injured almost 1,000.

A jury at Kingston crown court unanimously found Waheed Ali, 25, Sadeer Saleem, 28, and Mohammed Shakil, 32, all from Beeston, Leeds, not guilty of conspiring with the four bombers to cause explosions, after deliberating for eight days.

They are the only people to be charged over the attacks in 2005, which prompted the biggest criminal investigation in British history – more than 18,450 statements were taken and at least 37,000 exhibits were collected.

Ali and Shakil were, however, convicted of conspiracy to attend a place used for terrorist training. They were about to board a flight to Pakistan when they were arrested in 2007. The pair will be sentenced tomorrow afternoon.

The home secretary, Jacqui Smith, welcomed those guilty verdicts, which she said "clearly demonstrated the determined stance the UK takes against those suspected of involvement in terrorism".

As the verdicts were read out, Ali smiled broadly, Saleem wiped his eyes and Shakil leant forward, mouthing "thank you" to the jury. The trio had been retried after a jury failed to reach a verdict on the charges relating to the 7 July attacks last year after about three weeks of deliberations.

Survivors of the attacks and family members of those who died said today's verdicts strengthened the case for an independent inquiry into the bombings.

The end of the trial clears the way for the publication of a long-awaited report into whether the attacks could have been prevented, which is expected to be critical of the way MI5 and West Yorkshire police responded to earlier intelligence linking some of the suicide bombers with a group who were plotting to explode a series of huge fertiliser bombs.

The two key bombers, Mohammad Siddique Khan and Shehzad Tanweer, crossed MI5's radar several times in 2004 as the security service watched the gang that was later convicted of plotting to blow up Bluewater shopping centre in Kent and south London's Ministry of Sound nightclub.

Ali was also present when Khan and Tanweer met the leader of that cell, Omar Khyam, and Shakil and Khan trained with him at a camp in Pakistan in 2003.

But after the fertiliser plotters were arrested in March 2003, Khan and Tanweer, who had been judged to be peripheral figures because they only seemed interested in committing fraud to fund overseas jihad, were not followed again by M15 and were not identified by the service.

Khyam was referred to as "Ausman" during the trial for fear that revealing his true indentity to the jury would prejudice the case.

Graham Foulkes, whose 22-year-old son David worked for the Guardian in Manchester and was killed in the Edgware Road tube explosion, said: "For almost four years, we have been asking for an inquiry into what led up to 7/7.

"We are not looking for people to blame, but we also know that we have not been told the whole truth. We believe that crucial lessons need to be learned. If mistakes have been made, they should be put right, not covered up. This is not a witch-hunt, it is simply about saving lives."

Police have said they know others were involved in the attacks and believe there are still people in Beeston with significant information who have never come forward.

Deputy assistant commissioner John McDowall, the head of the Metropolitan police's counterterrorism command, said he believed others were involved in planning the attacks.

"I would urge anybody who has any information about 7/7 to come forward and contact police," he said. "I do understand that people may have concerns about the impact of giving us information, but it is the right thing to do."

Speaking about Ali and Shakil, he said: "These two men learned to fight at training camps attended by other terrorists. Mohammed Siddique Khan and Mohammed Shakil told other attendees that their aim was to fight in Afghanistan. They were proficient in the use of, and handling of, terrorist weapons and were certainly not enjoying a day out in a beautiful and mountainous area of Pakistan, as was suggested in court.

"Shakil himself accepted that the camp at Malakand was a serious business, whose purpose was to train willing volunteers to fight and kill in Afghanistan on behalf of the Taliban, a cause to which both he and Ali were, and remain, sympathetic.

"Ali and Shakil clearly associated with, and shared the terrorist beliefs of, the London bombers."

Ali, Saleem and Shakil spent two days in London with the bus bomber, Hasib Hussain, in December 2004 and were joined there by another of the attackers, Jermaine Lindsay, who killed 26 people on a Piccadilly line underground train.

The trio had denied the charges and said they were on a sightseeing trip. They went on the London Eye and visited the Natural History Museum and the London Aquarium as they travelled around the capital.

The prosecution alleged they conducted a "hostile reconnaissance" of potential targets, claiming it was "an important first step in what was, by then, a settled plan to cause explosions in the UK".

Interviewed by police shortly after the bombings, Ali, Saleem and Shakil distanced themselves from the bombers but, in the year that followed, DNA and fingerprint evidence linked them to the two bomb factories in the city and made them "persons of interest".

Detectives first realised the trio may have been to London with Hussain and Lindsay while analysing the details of 4,700 phone numbers and 90,000 calls. Cell site analysis, pinpointing the location of a mobile phone when a call is made, revealed that all five men had been in the capital on 16-17 December. The analysis allowed the group's movements across London to be mapped.

But there was no CCTV footage to show what they had been doing and no proof they had even been on the London underground, where three of the four bombs exploded.

The trio argued during the trial that the items carrying their DNA had been taken to the bomb factories by the bombers, not them.

The jury was warned not to think that they must be guilty just because they were friends with the bombers, with whom they attended the same mosques, gyms and community organisations growing up in Beeston.

The Crown Prosecution Service later defended its decision to prosecute the three men and to go for a retrial following the first court case, although it "fully respected" the jury's verdict.

Sue Hemming, the head of the counterterrorism division, said: "Although there was no direct evidence that these men were involved in the terrible events of 7/7, we felt there was sufficient evidence to show they were involved in reconnaissance and planning for an attack of some kind and it was in the public interest that such a serious matter should be put before a court."

Saleem, who was cleared of all charges, called for an inquiry into his prosecution.

In a statement read by Imran Khan, his solicitor, on the steps of Kingston crown court, Saleem said: "I have lost over two years of my life which I will never get back. Even though I have been acquitted, some people will always connect me with these events.

"I want people to know I am totally innocent and I want there to be an inquiry into why I was prosecuted on the flimsiest of evidence. Nobody should be put through what I have gone through."